Last updated: 2019-03-01
Checks: 4 2
Knit directory: DNASeq/
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| Name | Class | Size |
|---|---|---|
| a | packageIQR | 2.3 Kb |
| alignMerge | cwlStepParam | 306.3 Kb |
| bwa | cwlParam | 25.2 Kb |
| bwaAlign | cwlStepParam | 125.7 Kb |
| dats | packageIQR | 2.3 Kb |
| f1 | InputParam | 2.8 Kb |
| f2 | InputParam | 2.8 Kb |
| f3 | InputParam | 2.8 Kb |
| fastqc | cwlParam | 13.8 Kb |
| featureCounts | cwlParam | 19.4 Kb |
| fq1 | list | 832 bytes |
| fq2 | list | 832 bytes |
| fq2ubamJson | cwlParam | 37.4 Kb |
| GAlign | cwlStepParam | 211.9 Kb |
| geneBody_coverage | cwlParam | 21.8 Kb |
| genePredToBed | cwlParam | 16.5 Kb |
| gtfToGenePred | cwlParam | 16.5 Kb |
| hapCall | cwlStepParam | 29.6 Kb |
| hapJson | cwlParam | 19.3 Kb |
| inputList | list | 3.5 Kb |
| jdCall | cwlStepParam | 129.5 Kb |
| jdJson | cwlParam | 28.3 Kb |
| markdup | cwlParam | 21.8 Kb |
| mc3 | cwlStepParam | 90.6 Kb |
| mergeBam | cwlParam | 18.4 Kb |
| mergeBamDup | cwlStepParam | 122.7 Kb |
| mvOut | cwlParam | 13.4 Kb |
| o1 | OutputParam | 2.3 Kb |
| o2 | OutputParam | 2.3 Kb |
| o2a | OutputParam | 2.3 Kb |
| o2b | OutputParam | 2.3 Kb |
| o2c | OutputParam | 2.3 Kb |
| o3 | OutputParam | 2.3 Kb |
| o4 | OutputParam | 2.4 Kb |
| o5 | OutputParam | 2.4 Kb |
| o6 | OutputParam | 2.4 Kb |
| o7 | OutputParam | 2.3 Kb |
| o8 | OutputParam | 2.3 Kb |
| p1 | InputParam | 2.8 Kb |
| p10 | InputParam | 2.8 Kb |
| p11 | InputParam | 2.8 Kb |
| p12 | InputParam | 2.8 Kb |
| p13 | InputParam | 2.8 Kb |
| p2 | InputParam | 2.8 Kb |
| p3 | InputParam | 2.8 Kb |
| p4 | InputParam | 2.8 Kb |
| p5 | InputParam | 2.8 Kb |
| p6 | InputParam | 2.8 Kb |
| p7 | InputParam | 2.8 Kb |
| p8 | InputParam | 2.8 Kb |
| p9 | InputParam | 2.8 Kb |
| paramList | list | 576 bytes |
| read_distribution | cwlParam | 16.6 Kb |
| req1 | list | 416 bytes |
| req2 | list | 416 bytes |
| req3 | list | 416 bytes |
| rgs | list | 880 bytes |
| rnaseq_Sf | cwlStepParam | 315.6 Kb |
| rscripts | character | 816 bytes |
| RSeQC | cwlStepParam | 126 Kb |
| runWDL | cwlParam | 21.7 Kb |
| s1 | stepParam | 19.5 Kb |
| s2 | stepParam | 44.2 Kb |
| s3 | stepParam | 20.1 Kb |
| s4 | stepParam | 19.5 Kb |
| s5 | stepParam | 28.1 Kb |
| s6 | stepParam | 133.4 Kb |
| sam2bam | cwlParam | 13.9 Kb |
| samples | list | 592 bytes |
| samtools_flagstat | cwlParam | 13.8 Kb |
| samtools_index | cwlParam | 14.4 Kb |
| sortBam | cwlParam | 13.8 Kb |
| STAR | cwlParam | 32.2 Kb |
| ubam2bamJson | cwlParam | 16.6 Kb |
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Untracked files:
Untracked: analysis/Rcwl_DNASeq_Align.Rmd
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Untracked: analysis/Rcwl_GATK4.Rmd
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Untracked: test.bam
Untracked: tmpl1.json
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The GATK4 best practices for germline short variant discovery was implemented with Workflow Description Language (WDL), which is similar to cwl and requires cromwell to run the pipelines.
Here is the details of the pipeline: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145
Germline short variant discovery (SNPs + Indels)
The germline pipelines include 4 steps in WDL, paired fastq to ubam, GATK alignment, variant calling by HaplotypeCaller and joint genotyping. We wrapped the GATK pipelines to 3 steps using Rcwl for different numbers of computing nodes requirements. The wrapped pipelines can help to assign inputs to the input JSON templates and glob results from the cromwell outputs.
First, we need to load the packages and pipelines.
library(Rcwl)
library(RcwlPipelines)
data("GAlign")
data("hapCall")
data("jdCall")
We wrapped the steps from raw fastqs to analysis-ready BAM file into GAlign pipeline. Here is the short summary of the pipeline.
short(GAlign)
inputs:
- fastq1
- fastq2
- readGroup
- sampleName
- library
- platunit
- platform
- center
- tmpl1
- wdl1
- tmpl2
- wdl2
- cromwell
outputs:
- bamlog
- outdir
steps:
- fqJson
- fq2ubam
- ubam2bamJson
- align
- mvOut
For the inputList, we need to assign the fastqs files and read groups for each sample. The inputs can be multiple items separated by comma if there are more than one read groups for each sample. The input templates and WDL scripts can be assigned in the paramList and the reference and other GATK bundle files should be changed to your local version of files accordingly in the local json files. The path to the cromwell binary file is also required. Here is an example.
tmpl1 <- system.file(package="RcwlPipelines", "GATK4/seq-format-conversion/paired-fastq-to-unmapped-bam.inputs.json")
tmpl2 <- system.file(package="RcwlPipelines", "GATK4/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.local.json")
wdl1 <- system.file(package="RcwlPipelines", "GATK4/seq-format-conversion/paired-fastq-to-unmapped-bam.wdl")
wdl2 <- system.file(package="RcwlPipelines", "GATK4/gatk4-data-processing/processing-for-variant-discovery-gatk4.wdl")
inputList <- list(fastq1=list(normal="/home/qhu/workspace/projects/RPipe/data/DNASeq/data/normal_1.fq",
tumor="/home/qhu/workspace/projects/RPipe/data/DNASeq/data/tumor_1.fq"),
fastq2=list(normal="/home/qhu/workspace/projects/RPipe/data/DNASeq/data/normal_2.fq",
tumor="/home/qhu/workspace/projects/RPipe/data/DNASeq/data/tumor_2.fq"),
readGroup=list("normal.1", "tumor.1"),
sampleName=list("normal", "tumor"),
library=list("normal", "tumor"),
platunit=list("normal", "tumor"),
platform=list("illumina", "illumina"),
center=list("rpccc", "rpccc"))
paramList <- list(tmpl1=tmpl1,
wdl1=wdl1,
tmpl2=tmpl2,
wdl2=wdl2,
cromwell="/mnt/lustre/users/qhu/software/cromwell-36.jar")
r1 <- runCWLBatch(GAlign, outdir="output/BAM", inputList, paramList,
BatchtoolsParam(workers = 2, cluster="sge",
template = "/rpcc/bioinformatics/sge_centos7.tmpl",
resources = list(threads = 16,
queue = "centos7.q")),
stderr="")
The outputs were globbed from the cromwell execution folder.
list.files("output/BAM/normal", recursive = TRUE)
[1] "output/normal.hg38.bai"
[2] "output/normal.hg38.bam"
[3] "output/normal.hg38.bam.md5"
[4] "output/normal.hg38.duplicate_metrics"
[5] "output/normal.hg38.recal_data.csv"
[6] "processing-for-variant-discovery-gatk4.wdl.log"
This step takes the BAM files as input and each BAM file will be assigned to different computing node. Also the json template file need to be modified to the correct GATK bundle paths at first.
wdl3 <- system.file(package="RcwlPipelines", "GATK4/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.wdl")
tmpl3 <- system.file(package="RcwlPipelines", "GATK4/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.inputs.local.json")
bams <- list(normal = normalizePath("output/BAM/normal/output/normal.hg38.bam"),
tumor = normalizePath("output/BAM/tumor/output/tumor.hg38.bam"))
inputList <- list(bam = bams)
paramList <- list(intervals = normalizePath("output/interval.txt"),
cromwell = "/mnt/lustre/users/qhu/software/cromwell-36.jar",
wdl = wdl3,
tmpl = tmpl3)
r2 <- runCWLBatch(hapCall, outdir="output/GATK", inputList, paramList,
BatchtoolsParam(workers = 2, cluster="sge",
template = "/rpcc/bioinformatics/sge_centos7.tmpl",
resources = list(threads = 16,
queue = "centos7.q")),
stderr="")
Here are the outputs:
list.files("output/GATK/normal", recursive = TRUE)
[1] "haplotypecaller-gvcf-gatk4.wdl.log"
[2] "output/normal.hg38.g.vcf.gz"
[3] "output/normal.hg38.g.vcf.gz.tbi"
The joint genotyping step will combine the gvcf files and then call variants in all samples, so only one computing node is required. Multiple values or files of the samples need to be pasted by comma for each input in the inputList. The paths of the local bundle files are also need to be added to the json template file.
wdl4 <- system.file(package="RcwlPipelines", "GATK4/gatk4-germline-snps-indels/joint-discovery-gatk4-local.wdl")
tmpl4 <- system.file(package="RcwlPipelines", "GATK4/gatk4-germline-snps-indels/joint-discovery-gatk4-local.hg38.wgs.inputs.json")
inputList <- list(sampleName = list(test="normal,tumor"),
gvcf = list(test="/home/qhu/workspace/projects/RPipe/data/DNASeq/output/GATK/normal/output/normal.hg38.g.vcf.gz,/home/qhu/workspace/projects/RPipe/data/DNASeq/output/GATK/tumor/output/tumor.hg38.g.vcf.gz"))
paramList <- list(callsetName = "test",
intervals = "/home/qhu/workspace/projects/RPipe/data/DNASeq/output/interval.21.interval_list",
unpadded_intervals = "/home/qhu/workspace/projects/RPipe/data/DNASeq/output/interval.21.intervals",
tmpl = tmpl4,
cromwell = "/mnt/lustre/users/qhu/software/cromwell-36.jar",
wdl = wdl4)
r3 <- runCWLBatch(jdCall, outdir="output/GATK", inputList, paramList,
BatchtoolsParam(workers = 1, cluster="sge",
template = "/rpcc/bioinformatics/sge_centos7.tmpl",
resources = list(threads = 16,
queue = "centos7.q")),
stderr="")
Here are the final outputs:
list.files("output/GATK/test", recursive = TRUE)
[1] "joint-discovery-gatk4-local.wdl.log"
[2] "output/out.intervals"
[3] "output/test.variant_calling_detail_metrics"
[4] "output/test.variant_calling_summary_metrics"
[5] "output/test.vcf.gz"
[6] "output/test.vcf.gz.tbi"
sessionInfo()
R version 3.5.2 Patched (2018-12-31 r75935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)
Matrix products: default
BLAS: /home/qhu/usr/R-3.5/lib64/R/lib/libRblas.so
LAPACK: /home/qhu/usr/R-3.5/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RcwlPipelines_0.99.0 testthat_2.0.1 BiocStyle_2.10.0
[4] rmarkdown_1.11 knitr_1.21 usethis_1.4.0
[7] devtools_2.0.1 Rcwl_0.99.14 S4Vectors_0.20.1
[10] BiocGenerics_0.28.0 yaml_2.2.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-0 rprojroot_1.3-2 fs_1.2.6
[4] rstudioapi_0.9.0 roxygen2_6.1.1 remotes_2.0.2
[7] xml2_1.2.0 pkgload_1.0.2 jsonlite_1.6
[10] workflowr_1.2.0 shiny_1.2.0 DiagrammeR_1.0.0
[13] BiocManager_1.30.4 readr_1.3.1 compiler_3.5.2
[16] backports_1.1.3 assertthat_0.2.0 lazyeval_0.2.1
[19] cli_1.0.1 later_0.8.0 visNetwork_2.0.5
[22] htmltools_0.3.6 prettyunits_1.0.2 tools_3.5.2
[25] igraph_1.2.4 gtable_0.2.0 glue_1.3.0
[28] dplyr_0.8.0.1 batchtools_0.9.11 rappdirs_0.3.1
[31] Rcpp_1.0.0 rgexf_0.15.3 xopen_1.0.0
[34] debugme_1.1.0 xfun_0.5 stringr_1.4.0
[37] ps_1.3.0 mime_0.6 XML_3.98-1.17
[40] scales_1.0.0 hms_0.4.2 promises_1.0.1
[43] RColorBrewer_1.1-2 memoise_1.1.0 gridExtra_2.3
[46] ggplot2_3.1.0 downloader_0.4 rcmdcheck_1.3.2
[49] stringi_1.3.1 highr_0.7 Rook_1.1-1
[52] desc_1.2.0 checkmate_1.9.1 pkgbuild_1.0.2
[55] BiocParallel_1.16.6 rlang_0.3.1 pkgconfig_2.0.2
[58] commonmark_1.7 evaluate_0.13 purrr_0.3.0
[61] htmlwidgets_1.3 processx_3.2.1 tidyselect_0.2.5
[64] plyr_1.8.4 magrittr_1.5 bookdown_0.9
[67] R6_2.4.0 base64url_1.4 pillar_1.3.1
[70] withr_2.1.2 tibble_2.0.1 crayon_1.3.4
[73] viridis_0.5.1 progress_1.2.0 grid_3.5.2
[76] data.table_1.12.0 git2r_0.24.0 callr_3.1.1
[79] influenceR_0.1.0 digest_0.6.18 xtable_1.8-3
[82] tidyr_0.8.2 httpuv_1.4.5.1 brew_1.0-6
[85] munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1